I do overhead-projector shadow puppetry, and I do use both fishing line
and the paints used to make fake stained glass. So for the joints I make
an incision with a needle and then I knot the fishing line on one end and
pull it through the hole and then I tie a knot on the other end. I have
never had the knot pull through the hole, though I am always afraid it might.
So far, the holes seem to stay at their original size and the knots seem
to stay knotted.

As far as the paint, I have only painted small portions of the puppets
and for this the stained-glass paints seem fine -- the streaking does not
become a problem. For what it's worth, I cover the surface first with
a coat of shellac (or whatever the lacquer equivalent of this is called).
I let this dry, and then I use the paint over it. I am not sure whether
this has any practical effects or I just sucked it out of thin air.
I also use the shellac to cover the printed surfaces of the puppets (the
"printing" is, in my case, via photocopy) to prevent the print from
flaking off.

Another problem with acetate puppets is the question of glue. I have never
found a really good glue that works between two pieces of acetate and does
not have strange optical effects. And then there is the question of what
glue to use to glue transparent paper to acetate. And then there is the
question of what paints to use on transparent fabric of one wants to make
projections involving patterned fabrics...